[Ontology-editors] CC organization question for xps

[Midori Harris]

comments on comments

On Mon, 17 Nov 2008, David Hill wrote:

> Comments follow.
>> I have a suggestion and question about the CC organization terms that are 
>> relevant to XPs ...
>> 
>> Several of us agreed recently that all cellular components are anatomical 
>> structures. For the xp set I'm looking at -- 
>> biological_process_xp_cellular_component.* -- I can put in more specific 
>> genus terms for several xp defs if I add the relationship:
>> 
>> GO:0022607 cellular component assembly is_a GO:0048646 anatomical structure 
>> formation
>
> Would it make sense then to have an exact synonym of cellular component 
> formation as an exact synonym of cellular component assembly?

sure; want me to add?

>> 
>> It might also be good (though less pressing for my xps) to add a parent in 
>> the anatomical structure branch of BP for GO:0016043 cellular component 
>> organization. I'm not sure whether GO:0048532 anatomical structure 
>> arrangement exactly fits the bill, though. The definitions don't quite 
>> match up, in that GO:0048532 is restricted to "the configuration of the 
>> constituent parts of an anatomical structure" and so covers only the 
>> "arrangement of constituent parts" part of the GO:0016043 def, not the 
>> formation or disassembly. (I also don't quite understand how GO:0048532 can 
>> have 'structural organization' as an exact synonym when the more restricted 
>> phrase 'anatomical structure organization' is a broad synonym.)
>
> The anatomical terms follow the morphogenesis paradigm. Morphogenesis has 3 
> parts, formation, organization and regression. It seems that these would be 
> exactly parallel with assembly, arrangement and disassembly. I really would 
> prefer not to rearrange the way the anatomical structure morphogenesis terms 
> are organized since Tanya and I put a LOT of thought into this.

OK; it was just the inconsistency between CC org and anatomical structure 
stuff that I spotted and thought should be resolved one way or another.

> I think 
> GO:0022607 is_a GO:0048646,

Yes, this is the relationship I proposed to add in my first email.

> GO:0016043 and GO:0032989 might be synonymous and redefined to be 
> parallel with morphogeneis, GO:0022411is_a GO:0060033.

I'm a little confused here -- do you mean that GO:0016043 (cellular 
component organization) and GO:0032989 (cellular structure morphogenesis) 
are synonymous with each other and should be merged? And we should add the 
relationship GO:0022411 (cellular component disassembly) is_a GO:0060033 
(anatomical structure regression)?

> There is currently no term that would be a CC counterpart of GO:0016043, 
> anatomical structure arrangement.

??? anatomical structure arrangement is GO:0048532. I agree that there's 
no CC counterpart at present.

m

> Perhaps we need to make a new term 
> cellular component arrangement. Note also that the defs will need to 
> change a bit since the formation, arrangement, and dissassembly would 
> all be a part of morphogenesis.
>
> David
>
>